Difference between revisions of "Skogsbergia lerneri"
| Line 13: | Line 13: | ||
| − | <p>>contig02168 length=583 numreads=7 gene=isogroup01241 status=isotig | + | <p>>contig02168 length=583 numreads=7 gene=isogroup01241 status=isotig</p> |
ATAAGATGAGGACACAGACACTGTTCCCcACACTCACACACATCAAGAaTACAGAACTCCAGGgTCTCTCGGAaGTTCAC | ATAAGATGAGGACACAGACACTGTTCCCcACACTCACACACATCAAGAaTACAGAACTCCAGGgTCTCTCGGAaGTTCAC | ||
TTCCAAGCAGGAGATTTtGGATAGAGCCATCTCACACTTGTGATGGGCTTTCTGTCTCTGTGCTTTTGTGCAGGTTGGAG | TTCCAAGCAGGAGATTTtGGATAGAGCCATCTCACACTTGTGATGGGCTTTCTGTCTCTGTGCTTTTGTGCAGGTTGGAG | ||
| Line 21: | Line 21: | ||
aGGCGCCTTTTTtAACAGGAAGTTTGACCAATTTTCCATCAACCTTCACATCTTTtCTGCTGATGACTATGGTCGCTCCT | aGGCGCCTTTTTtAACAGGAAGTTTGACCAATTTTCCATCAACCTTCACATCTTTtCTGCTGATGACTATGGTCGCTCCT | ||
TtGAGTTCAAGTGTTACTcTAGCCACACTGgATACCCTGgcTCCcTTAtAGgTTGGTTCATtCTTtGtAATGACCTTCCA | TtGAGTTCAAGTGTTACTcTAGCCACACTGgATACCCTGgcTCCcTTAtAGgTTGGTTCATtCTTtGtAATGACCTTCCA | ||
| − | TTtGTTGGTCTTACAGTCtGCTG | + | TTtGTTGGTCTTACAGTCtGCTG |
Revision as of 22:07, 11 November 2011
Skogsbergia lerneri luciferase homolog
Skogsbergia lerneri is a non-luminescent myodocopid ostracod that lives in the Caribbean, from the same family (Cypridinidae) as multiple bioluminescent species.
To use Skogsbergia lerneri in the 'convergent luciferase' project, the goal is to isolate a homolog of the luciferase gene, and express the S. lerneri gene in cell culture to test whether it catalyzes a light reaction when mixed with luciferase.
Steps completed thus far:
- 454 Sequencing of specimens from Florida Keys was completed. The sequencing was done from Median Eyes and Compound Eyes only.
(We expect homologs to be expressed at the upper lip, the site of luciferase excretion; so eyes may not be the best tissue for finding luciferase homologs.)
- The 454 transcriptome is assembled in Galaxy, with a shared history called Skogsbergia Eyes [1]
- A blast search, available in the Galaxy history, yields 2 contigs.
- contig02168 - when blasted against GenBank hits vitellogenin
- contig00156 - when blasted against GenBank hits kielins and mucins
>contig02168 length=583 numreads=7 gene=isogroup01241 status=isotig
ATAAGATGAGGACACAGACACTGTTCCCcACACTCACACACATCAAGAaTACAGAACTCCAGGgTCTCTCGGAaGTTCAC TTCCAAGCAGGAGATTTtGGATAGAGCCATCTCACACTTGTGATGGGCTTTCTGTCTCTGTGCTTTTGTGCAGGTTGGAG GAGGAGGTGgTGGGATACCACAGTCTTTtCCATGTAGATTCTTCTTGTGTAAGGCATCTTTATCCTTTGCCATCGCTTGG TCATCCTTTGGATTCTTGTCATAAGTTCCACACAGGCCACAAGTTTTtCCTTtCCATTTTGCTTCCACTACCACTTTGAT GTGCATACGTTgaTCATaGgAAACGtCTACTCCAAgTTtGGTTTcgAtCTTCACTTCTCTTCCTTTCTTCGTgaTGgAAA aGGCGCCTTTTTtAACAGGAAGTTTGACCAATTTTCCATCAACCTTCACATCTTTtCTGCTGATGACTATGGTCGCTCCT TtGAGTTCAAGTGTTACTcTAGCCACACTGgATACCCTGgcTCCcTTAtAGgTTGGTTCATtCTTtGtAATGACCTTCCA TTtGTTGGTCTTACAGTCtGCTG
